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- PDB-7b6u: Sheep Polyomavirus VP1 in complex with 5 mM Forssman antigen pent... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7b6u | ||||||
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Title | Sheep Polyomavirus VP1 in complex with 5 mM Forssman antigen pentaose and 20 mM 6'-sialyllactosamine | ||||||
![]() | Capsid protein VP1 | ||||||
![]() | VIRAL PROTEIN / polyomavirus / capsid protein / VP1 / glycan complex | ||||||
Function / homology | ![]() T=7 icosahedral viral capsid / host cell nucleus / virion attachment to host cell / structural molecule activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rustmeier, N.H. / Stehle, T. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A novel and highly specific Forssman antigen-binding protein from sheep polyomavirus Authors: Rustmeier, N.H. / Silva, L.M. / Di Maio, A. / Mueller, J.C. / Herrmann, A. / Feizi, T. / Liu, Y. / Stehle, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 580.3 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 7.4 MB | Display | ![]() |
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Full document | ![]() | 7.4 MB | Display | |
Data in XML | ![]() | 115.5 KB | Display | |
Data in CIF | ![]() | 163.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7b6sC ![]() 7b6tC ![]() 7b6vC ![]() 6y61S C: citing same article ( S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 10 molecules AAABBBCCCDDDEEEFFFGGGHHHIIIJJJ
#1: Protein | Mass: 30577.434 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 3 types, 16 molecules ![](data/chem/img/SIA.gif)
#2: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose #3: Polysaccharide | 2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)- ...2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose Source method: isolated from a genetically manipulated source #6: Sugar | ChemComp-SIA / | |
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-Non-polymers , 4 types, 2044 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-PEG / #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.5 Å3/Da / Density % sol: 64.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: KSCN, PEG 3350 |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N | ||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 13, 2019 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 1.00004 Å / Relative weight: 1 | ||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.9→49.48 Å / Num. obs: 325151 / % possible obs: 99.8 % / Redundancy: 5.3 % / Biso Wilson estimate: 31.3 Å2 / CC1/2: 0.996 / Rrim(I) all: 0.1461 / Net I/σ(I): 9.46 | ||||||||||||||||||
Reflection shell | Resolution: 1.9→2.02 Å / Mean I/σ(I) obs: 1.33 / Num. unique obs: 51994 / CC1/2: 0.441 / Rrim(I) all: 1.223 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6Y61 Resolution: 1.901→49.47 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.96 / Cross valid method: FREE R-VALUE / ESU R: 0.019 / ESU R Free: 0.019 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.683 Å2
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Refinement step | Cycle: LAST / Resolution: 1.901→49.47 Å
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Refine LS restraints |
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LS refinement shell |
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